Pinned Repositories
ampseer
Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.
domainator
A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.
EM-seq
Tools and Data related to Enzymatic Methylation Sequencing
mark-nonconverted-reads
This program examines a BAM or SAM stream for reads that contain multiple Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints summary information to stderr.
methylation_tools
A few tools for manipulating methylation call files
nebnext-single-cell-rna-seq
Adapter trimming directions for NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina
plate-map
A flexible tool for defining the contents of 96 well plates.
primer_monitor
a service to allow people to register primers to be monitored for intersecting variants and be notified if new variants arise
seq-results-deprecated
Deprecated: Web interface to manage a database of sequence results (merged into ngs-aggregate-results)
VarSkip
VarSkip multiplex PCR designs for SARS-CoV-2 sequencing
New England Biolabs Inc.'s Repositories
nebiolabs/plate-map
A flexible tool for defining the contents of 96 well plates.
nebiolabs/EM-seq
Tools and Data related to Enzymatic Methylation Sequencing
nebiolabs/ampseer
Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.
nebiolabs/VarSkip
VarSkip multiplex PCR designs for SARS-CoV-2 sequencing
nebiolabs/domainator
A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.
nebiolabs/mark-nonconverted-reads
This program examines a BAM or SAM stream for reads that contain multiple Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints summary information to stderr.
nebiolabs/iiMS_InfluenzaA
NEBNext iiMS Influenza A Library Prep for ONT
nebiolabs/picard_bcl_to_fastq
Demultiplexes a MiSeq, NextSeq or HiSeq run using Picard's IlluminaBasecallsToFastq
nebiolabs/seq-results-deprecated
Deprecated: Web interface to manage a database of sequence results (merged into ngs-aggregate-results)
nebiolabs/tasmanian-mismatch
Analysis of artifacts in high throughput sequencing data from genomic DNA.
nebiolabs/opentrons
Collection of scripts which can be used in relation to Opentrons OT-2 Liquid Handling Robot
nebiolabs/uncleShiny
A dashboard for Unchained Labs Uncle data visualization written in R using Shiny.
nebiolabs/artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
nebiolabs/bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
nebiolabs/Cas-PAM-cleavage-analysis
nebiolabs/datasets-sars-cov-2
nebiolabs/domainator_examples
Advanced examples of how to use the Domainator bioinformatics software suite
nebiolabs/fatools
A Python library for performing DNA fragment-analysis
nebiolabs/FFPE_nextflow_workflow
Workflow to analyze FFPE ngs data
nebiolabs/formtastic
A Rails form builder plugin with semantically rich and accessible markup.
nebiolabs/galaxytools
:microscope::books: Galaxy Tool wrappers
nebiolabs/iwc
Intergalactic Workflow Commission
nebiolabs/low_bismap_methyl_calls
Tools to assess called methylation in low mappability regions (as defined by bismap). Aligner MapQ does not always align with low mappability
nebiolabs/neb-galaxy-workflows
Galaxy Workflows
nebiolabs/ngslite
Light-weight functions for next-generation sequencing (NGS) data analysis
nebiolabs/poreCov
SARS-CoV-2 workflow for nanopore sequence data
nebiolabs/primer-schemes
Primer schemes for real-time genome epidemiology
nebiolabs/rsvAB-sequencing
NEBNext RSV A/B Multiplex PCR sequencing primers
nebiolabs/unclePy
A parser for Unchained Labs Uncle HDF5 binary files written in Python.
nebiolabs/usegalaxy-tools
usegalaxy.* common tools